7AVI

Crystal structure of SOS1 in complex with compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

One Atom Makes All the Difference: Getting a Foot in the Door between SOS1 and KRAS.

Ramharter, J.Kessler, D.Ettmayer, P.Hofmann, M.H.Gerstberger, T.Gmachl, M.Wunberg, T.Kofink, C.Sanderson, M.Arnhof, H.Bader, G.Rumpel, K.Zophel, A.Schnitzer, R.Bottcher, J.O'Connell, J.C.Mendes, R.L.Richard, D.Pototschnig, N.Weiner, I.Hela, W.Hauer, K.Haering, D.Lamarre, L.Wolkerstorfer, B.Salamon, C.Werni, P.Munico-Martinez, S.Meyer, R.Kennedy, M.D.Kraut, N.McConnell, D.B.

(2021) J Med Chem 64: 6569-6580

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01949
  • Primary Citation of Related Structures:  
    7AVI, 7AVL, 7AVS, 7AVT, 7AVU, 7AVV

  • PubMed Abstract: 

    KRAS, the most common oncogenic driver in human cancers, is controlled and signals primarily through protein-protein interactions (PPIs). The interaction between KRAS and SOS1, crucial for the activation of KRAS, is a typical, challenging PPI with a large contact surface area and high affinity. Here, we report that the addition of only one atom placed between Y884 SOS1 and A73 KRAS is sufficient to convert SOS1 activators into SOS1 inhibitors. We also disclose the discovery of BI-3406 . Combination with the upstream EGFR inhibitor afatinib shows in vivo efficacy against KRAS G13D mutant colorectal tumor cells, demonstrating the utility of BI-3406 to probe SOS1 biology. These findings challenge the dogma that large molecules are required to disrupt challenging PPIs. Instead, a "foot in the door" approach, whereby single atoms or small functional groups placed between key PPI interactions, can lead to potent inhibitors even for challenging PPIs such as SOS1-KRAS.


  • Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Son of sevenless homolog 1
A, B
487Homo sapiensMutation(s): 0 
Gene Names: SOS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07889 (Homo sapiens)
Explore Q07889 
Go to UniProtKB:  Q07889
PHAROS:  Q07889
GTEx:  ENSG00000115904 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07889
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S2Q (Subject of Investigation/LOI)
Query on S2Q

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-propan-2-yl-~{N}-[(1~{R})-1-(3-sulfamoylphenyl)ethyl]-[1,2]oxazolo[5,4-b]pyridine-5-carboxamide
C18 H20 N4 O4 S
HRWBSXDFUWMVHN-LLVKDONJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.277α = 90
b = 84.441β = 90.12
c = 174.838γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Research Promotion AgencyAustria854341, 861507, 867897 and 874517

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description